A Python Package for Protein Dynamics Analysis
New Features:
Bug Fixes and Improvements:
Full Changelog: https://github.com/prody/ProDy/compare/v2.4.0...v2.4.1
New Features:
Bug Fixes and Improvements:
New Contributors:
Full Changelog: https://github.com/prody/ProDy/compare/v2.3.1...v2.4.0
Bug Fixes and Improvements:
Full Changelog: https://github.com/prody/ProDy/compare/v2.3.0...v2.3.1
New Features:
Bug Fixes and Improvements:
Full Changelog: https://github.com/prody/ProDy/compare/v2.2.0...v2.3.0
Bug Fixes and Improvements:
Updates to :function:`.parseScipionModes`` to use sqlite and xmd metadata files and handle eigenvalues
Actual fix to logging so LOGGER.progress doesn't override logging level
Updates to the PCA app to better handle number of modes for Scipion
New arguments sparse, kdtree and turbo for :class:.ClustENM
, allowing
better control of ANM calculations.
Another bug fix for mmCIF header parsing
Bug fix for parsing CONECT bond records from PDB files
Full Changelog: https://github.com/prody/ProDy/compare/v2.1.2...v2.2.0
.showRMSFlucts
and :function:.calcRMSFlucts
for root-mean-square fluctuations.showAtomicLines
for overlaying multiple chainsFull Changelog: https://github.com/prody/ProDy/compare/v2.1.1...v2.1.2
New Features:
Integration with Scipion
New functions :function:.parseScipionModes
, :function:.writeScipionModes
and :function:.calcScipionScore
New argument --export-scipion (-S) in prody apps
Other
Added :function:.assignBlocks
for assigning blocks for RTB
Added mmCIF header parsing to create the same header dictionary as PDB header, including secstr information and biomolecular assembly building
New arguments for prody apps, including altloc, zeros, sparse, kdtree and turbo
Bug Fixes and Improvements:
Improvement to cealign mapping to be faster for protein only alignment
Bug fix for writing psf files
Full Changelog: https://github.com/prody/ProDy/compare/v2.0.2...v2.1.0
New Features:
Added :function:.realignModes
for comparing sets of modes calculated on unaligned
structures
New option by_time in :function:.showProjection
, allowing projections onto 1 PC
and the frames sampled over the time course of a simulation or the conformers in an ensemble.
Updates to ClustENM(D) to use latest and more efficient OpenMM version, 7.6
New :function:.parseGromacsModes
for parsing NMA and PCA modes calculated in Gromacs,
allowing the use of all-atom force fields and more efficient handling of large trajectories
Bug Fixes and Improvements:
Bug fixes to searchPfam and fetchPfamMSA, which no longer worked due to some security change.
Bug fix to Ensembles and Conformations for weights being indexed twice
Bug fix to --quiet option of apps that fixes the VMD ProDy interface
General documentation and error improvements
New Features:
Added :function:.calcRWSIP
for comparing sets of modes
New methods to convert :class:.Atom
, :class:.Atomic
and :class:.EMDMAP
to TEMPy objects, allowing calculations such as cross-correlation coefficient (CCC)
to EM maps.
Added :func:.calcDynamicFlexibilityIndex
and :func:.calcDynamicCouplingIndex
for further interpretation of PRS results.
Reinstated the option of using forces in PRS as in ProDy v1.8 (turbo=**False**
)
Added GitHub Actions Continuous Integration in place of Travis.
Bug Fixes and Improvements:
Compatibility and bug fixes for various functions, including pyparsing for selections.
Extended :class:.AdaptiveANM
to work with other models including explicit membrane
ANM, :class:.exANM
.
Improved capabilities for fetching and parsing mmCIF and EMD files.
Improved handling of residue and serial numbers including hexadecimal and hybrid36 formats.
Consistency fixes.
More non-standard amino acids (MEN, CSB, CME).
Full Changelog: https://github.com/prody/ProDy/compare/v2.0...v2.0.1